According to many
reliable reports appearing in the most reliable works of Hadīth like Sahīh
of Bukhārī and Sahīh of Muslim the Holy Prophet (sws) used to do
Raf‘u’l-yadayn (raising hands up to one’s shouders) when starting the
prayer, going to Ruku‘, standing from it, and standing after saying
Tashahhud. So I am confused as to why we are not supposed to do
Raf‘u’l-yadayn on other occasion besides starting the prayer when the Holy
Prophet (sws) did?

Answer:

The entire
structure of prayer was taught by the Holy Prophet (sws) to the entire
generation of the companions. All the people of the time of the Holy Prophet
(sws) must have known the exact method of the prayer. This structure has
been reported down by the collectivity of the Muslims without a break. You
know that people never stopped praying and the act of praying is not a
concealed one. This has always been a living tradition among the Muslim
community. Thus we have the form of the prayer exactly as the Holy Prophet (sws)
left it with us. It has been preserved and reported down through the most
reliable source of knowledge. This profoundly established practice is
countered by a couple of individual reports. We cannot question the
authenticity of the report transmitted by the generations of the Muslims
Ummah by the individual reports. We are bound to give some explanation to
the individual reports appearing in Sahīh of Bukhārī and other works of
Hadīth. I think the reporters who transmitted the reports must have reported
some previous practice of the Holy Prophet (sws) which he abandoned and left
the prayer in the final and ultimate form as it is with us. However, it
should be noted that this also indicates to the fact that the practice of
raising both hands at different occasions (other than at the beginning of
the prayer) is not a necessary part of the prayer. That is why we see that
the Prophet (sws) after initially doing it later abandoned it but did not
make sure to eliminate it from the practice.